The Islands were already known to Mediterranean Classical cultures, but the Archipelago was rediscovered and visited by Genovese, Majorcan, Portuguese and French sailors during the 13^th and 14^th centuries. Under the auspices of the Castilian crown, Europeans conquered the Canary Islands during the 15^th century, beginning with Lanzarote in 1402 and finishing with Tenerife in 1496. The conquest was rather violent because the Guanches often fought fiercely against the invaders. Even islands such as Lanzarote or Gomera, which pacifically received the first Norman and Castilian expeditions, were the scene of violent revolts because the natives were enslaved in large numbers to defray the cost of the military expeditions. In retaliation, the rebels, mainly men, were killed and massively deported by the conquerors [1].

There are several questions about the past and present of the Guanches that have attracted the curiosity of scientists since the 19^th century. They refer to the time(s) and way(s) they arrived on the islands, their geographic origin, and whether their descendants persist in the present-day population [2]. The oldest human settlement seems to be no earlier than the first millennium B.C., according to absolute C¹⁴ dating [3]. Coalescence age estimates obtained from mitochondrial DNA (mtDNA) [4] and Y-chromosome [5] putative founder lineages concord with archeological results.

As the islands were never connected with the African Continent, they had to be reached by sea. Their inhabitants did not supposedly have seafaring skills and communication among islands was thus absent at the time of the Spanish conquest. This poses the unresolved dilemma of whether the first settlers reached the islands by themselves and after that forgot their sailing skills or if they were transported to the islands by another maritime people [6].

From the beginning of the conquest, Guanche dialects and customs were found to be related to those of their N African Berber neighbors. Since then, anthropological, archeological and linguistic studies have provided further support to the N African origin of the indigenous population [7]. Furthermore, the different human types discovered and the heterogeneity of their cultural remains again points to the possibility of successive arrivals of N African settlers [8-13].

In spite of the aggressive conquest and subsequent massive European immigration and North and sub-Saharan African slave importation to the islands, historians estimated that approximately two-thirds of the Canary population were Africans and aborigines at the end of the 16^th century [14]. Moreover, osteological studies comparing aboriginal remains and modern rural populations, support the persistence of indigenous traits in the current population [10,15].

From the genetic perspective, strong evidence in support of a N African origin of the indigenous ancestors and their present-day persistence was only obtained when uniparental genetic markers were analyzed. Mitochondrial DNA (mtDNA) lineages, belonging to the U6 haplogroup [16], and Y-chromosome haplotypes of the E1b1b1b haplogroup, characterized by the M81 marker [17], both with a clear Berber origin, were detected in the Canary islanders at a significantly higher presence than in Iberians, their main colonizers [4,5]. In addition, admixture analysis taking the Iberians, Northwest and sub-Saharan West African populations as parental sources of the present-day Canary population, showed that the indigenous contribution was estimated to be 33% of maternal lineages [4] and only 7% for paternal lineages [5]. This strong sexual asymmetry was explained by a sociological bias favoring matings between Iberian males and indigenous females, and the greater indigenous male mortality during the Conquest [2]. Accordingly, intermediate admixture estimates were obtained when autosomal markers were used [18,19]. It is also worth mentioning that the detection of significant correlations between relative frequencies and/or diversity values for mtDNA, CD4/Alu haplotypes and ABO gene data, and geographical distances of the islands from Africa were explained assuming only one main colonization event [4,18,19]. On the contrary, using Y-chromosome markers, two opposite correlations were found [5], which was explained by at least two independent waves of colonists from NW Africa, still detectable today. These genetic results, although congruent with previous anthropological, archeological and linguistic data, have not been free of criticism. It is well known that admixture values strongly depend on the appropriate choice of the parental populations. To extrapolate the unknown indigenous population from a NW African sample pool seems unsuitable, because although the mtDNA haplogrup U6 present in the Canary Islanders and in North Africa originates in the latter [20], the most abundant Canary sublineage, U6b1, is absent in NW Africa, and the most abundant U6a sublineages on that continent are very scarce in the archipelago [4,16,21] pointing to different N African sources. Moreover, the unquestionably N African lineages present in the present-day Canary population may not be wholly due to the indigenous heritage but to Iberian colonizers, since these lineages, albeit in low frequencies, are also present in Spain and Portugal [22,23]. Another possibility is that those U6 lineages present in the islands may derive from slaves brought from the NW African coast after the conquest. However, all these concerns vanished when mtDNA information was obtained directly from indigenous remains [24], and exhumed 17^th–18^th century remains from Tenerife [25]. The presence of U6b1 lineages and other presumed founder lineages were detected in both samples, confirming their prehispanic origin. In addition, the direct incorporation of the indigenous sample as a parental source of the admixed Canary Islands populations provided greater indigenous female component estimates (42–73%) than those based on the present-day NW African maternal gene pool (33–43%).

Compared to the original natives, the 17^th–18^th century historical sample mainly differs by harboring lower frequencies of NW African haplogroups (p < 0.05), such as E-M81 (11.9% vs 26.7%), E-M78 (11.9% vs 23.3%) and J-M267 (11.9% vs 16.7%), and higher frequencies for European haplogroups (p < 0.001) like R-M269 (42.9% vs 10.0%) or R-M173, (9.5% vs 0.0%). A notable exception was I-M170 because it was not detected in the historical sample, despite being moderately frequent in the aborigines (6.7%).

Different founder effects on different islands could be a plausible explanation, since all the natives carrying I-M170 were from Gran Canaria, whereas the historical sample was taken from Tenerife. Another difference between these two samples is the higher, albeit not significant, frequency of sub-Saharan lineages (7.1% vs 3.3%) in this historical population. However, these differences were not detected at mtDNA level [24,25], as the NW African haplogroup U6 (10.2% vs 10.0%) and the most abundant and widespread European haplogroup H (46.9% vs 52.1%) showed similar frequencies in both samples. The sharp and swift change observed for the indigenous male and female genetic pools can be satisfactorily explained if it is accepted that indigenous females were reproductively more successful after the conquest than males, who were displaced by male European colonizers. Although sampling bias and drift effects could also explain these differences, the genetic data corroborate historical chronicles that narrated frequent mass killings and deportations of mainly males during the conquest [1,9]. Even after that first violent period, the better social and economical position held by the Europeans continued to favor their mating with indigenous females.

The asymmetric sexual evolution of the mixed population is also corroborated when quantitative admixture estimates are independently applied to their female and male genetic pools at different times (Table ​(Table3).3). The Iberian contribution to the male genetic pool increases from 63% in the 17^th–18^th centuries to 83% in the present-day population, which is accompanied by a parallel dropping of the male indigenous (31% vs 17%) and sub-Saharan (6% vs 1%) contributions. However, relative proportions in the female pool are strikingly constant for Iberians (48% vs 55%) and aborigines (40% vs 42%), from the 17^th–18^th centuries to the present [53], and only the sub-Saharan female contribution shows an important decrease (12% vs 3%).

These results indicate that indigenous males were negatively discriminated, not only at the beginning of the conquest but also afterwards. In the case of the sub-Saharan lineages, it seems that their mating disadvantage affected both sexes, although more so in males.